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. 2019 Oct 30;14(2):506–518. doi: 10.1038/s41396-019-0519-4

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — Three-year observation on within-host accumulation and phylogenetic relationship of TuMV in three infected Arabidopsis halleri plant patches. Temporal changes of accumulation (a) and negative-strand RNA (b) of TuMV in upper leaves of plant patches 1, 2, and 3 (P1, P2, and P3, respectively). Solid lines indicate smooth-spline fittings. Negative-strand RNA was detected by strand-specific RT-qPCR. Broken lines and dashed lines indicate spring/autumn equinoxes (SE/AE) and summer/winter solstices (SS/WS), respectively. The year periods (i.e., 2012, 2013, 2014, and 2015) were shown by white and grey shadings. c Phylogenetic relationships between TuMV strains detected from the three patches (red, black, and blue bars represent P1, P2, and P3, respectively) during the 3-year observation. One-time sample from additional six plants were included (P4‒P9; indicated by green coloured bars). Sample IDs were coded by plant patches and sampling dates. Previously reported five, four, and four strains selected from Japan, continental Asia, and Europe, respectively, were included, and the sequence of TuMV basal-B strain (IRNTRa6; whose original host is Rapistrum rugosum) was used as an outgroup (indicated by an orange coloured bar). The bootstrap values (% of 1000 replicates) are listed next to the branches. The bootstrap values in red supported the monophyly of virus sequences within plant patches 1, 2, and 3, and the value in blue supported the monophyly of virus sequences from the studied population